A novel SARS-CoV-2 related virus with complex recombination isolated from bats in Yunnan province, China

  1. Li-li Li
  2. Jing-lin Wang
  3. Xiao-hua Ma
  4. Jin-song Li
  5. Xiao-fei Yang
  6. Wei-feng Shi
  7. Zhao-jun Duan

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Abstract

A novel beta-coronavirus, SARS-CoV-2, emerged in late 2019 and rapidly spread throughout the world, causing the COVID-19 pandemic. However, the origin and direct viral ancestors of SARS-CoV-2 remain elusive. Here, we discovered a new SARS-CoV-2-related virus in Yunnan province, in 2018, provisionally named PrC31, which shares 90.7% and 92.0% nucleotide identities with SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment revealed that several genomic regions shared strong identity with SARS-CoV-2, phylogenetic analysis supported that PrC31 shares a common ancestor with SARS-CoV-2. The receptor binding domain of PrC31 showed only 64.2% amino acid identity with SARS-CoV-2. Recombination analysis revealed that PrC31 underwent multiple complex recombination events within the SARS-CoV and SARS-CoV-2 sub-lineages, indicating the evolution of PrC31 from yet-to-be-identified intermediate recombination strains. Combination with previous studies revealed that the beta-CoVs may possess more complicated recombination mechanism. The discovery of PrC31 supports that bats are the natural hosts of SARS-CoV-2.

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    SciScore for 10.1101/2021.03.17.435823: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the ethics committee of the CCDC, and was performed according to Chinese ethics, laws and regulations.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Prinseq-lite software (version 0.20.4) was used to remove lower quality reads, and Bowtie2 was used to align and map the filtered reads to the host reference genome.
    Bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    Mira (version 4.0.2) was used for de novo assembly of the clean reads.
    Mira
    suggested: (MIRA, RRID:SCR_010731)
    Both BLASTn and BLASTx of the BLAST+ package (version 2.2.30) were used to search against local viral nucleotide and protein databases.
    BLASTn
    suggested: (BLASTN, RRID:SCR_001598)
    BLASTx
    suggested: (BLASTX, RRID:SCR_001653)
    BLAST+
    suggested: (Japan Bioinformatics, RRID:SCR_012250)
    The E-value cut-off was set to 1 × 10−5 to maintain high sensitivity and a low false-positive rate when performing BLAST searches.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Phylogenetic and recombination analyses: The complete genome sequences of reference viruses were downloaded from GenBank (https://www.ncbi.nlm.nih.gov/) and GISAID (https://www.gisaid.org/).
    https://www.ncbi.nlm.nih.gov/
    suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)
    The complete genome of PrC31 was aligned with representative SARS-CoV, SARS-CoV-2 and SARSr-CoV using Mafft (v7.475).
    Mafft
    suggested: (MAFFT, RRID:SCR_011811)
    Phylogenetic analyses were performed with RaxML software (v8.2.11) using the general time reversible nucleotide substitution model, GAMMA distribution of rates among sites, and 1000 bootstrap replicates.
    RaxML
    suggested: (RAxML, RRID:SCR_006086)
    Potential recombination events were screened using RDP4 software and further analyzed by similarity plot using Sìmplot (v3.5.1) with potential major and minor parents.
    Sìmplot
    suggested: None

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.03.17.435823v2 on bioRxiv
  3. Version published to 10.1101/2021.03.17.435823v1 on bioRxiv